The Christian Democratic (CDU) politician is in the capital of Iraqi Kurdistan, Irbil, to meet with Kurdish president Masoud Barzani as well as German military personnel to discuss German arms deliveries.
The Kurds are fighting Islamic extremists Isis who have seized huge segments of northern Iraq and Syria in the past months.
Her visit is expected only to last a few hours. She is scheduled to visit a training facility the Bundeswehr has set up to teach Kurdish soldiers to use German-provided weapons.
An overnight flight from Leipzig to Iraq took off at 2am on Thursday morning, bringing 27 tonnes of weapons and ammunition 12 hours later than planned after a glitch with the transport plane. The cargo included 50 bazookas with ammunition, 520 guns, as well 20 machine guns.
Its first destination was Baghdad before heading to Irbil to deliver the equipment.
But a group of German military trainers who were supposed to arrive in Iraq before the delivery are still stuck in Bulgaria. They left Germany on Friday but had problems with their plane and were then refused permission to enter Iraq.
A total of 600 tonnes of weapons worth €70 million will be delivered by the Bundeswehr to 10,000 Kurdish Peshmerga fighters.
Von der Leyen cancelled a planned side trip to Baghdad, as the new Iraqi government has not yet appointed a defence minister and both Prime Minister Haidar al-Abadi and President Fuad Masum are attending the UN General Assembly in New York.